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A Survey of Molecular Communication in Cell Biology: Establishing a New Hierarchy for Interdisciplinary Applications

Dadi Bi, Apostolos Almpanis, Adam Noel, Yansha Deng, Robert Schober
2021 IEEE Communications Surveys and Tutorials  
Molecular communication (MC) engineering is inspired by the use of chemical signals as information carriers in cell biology.  ...  level; 4) the interpretation of information in cell signals and the realization of synthetic systems to store, process, and communicate molecular signals at the Local Data Abstraction level; and 5) applications  ...  multicellular organism, a hint on the importance of these communication channels.  ... 
doi:10.1109/comst.2021.3066117 fatcat:xd2o7fobtret3bc4vc5yqbckru

A Survey of Molecular Communication in Cell Biology: Establishing a New Hierarchy for Interdisciplinary Applications [article]

Dadi Bi, Apostolos Almpanis, Adam Noel, Yansha Deng, Robert Schober
2020 arXiv   pre-print
Molecular communication (MC) engineering is inspired by the use of chemical signals as information carriers in cell biology.  ...  To bridge this gap, this survey proposes a novel communication hierarchy for MC signaling in cell biology and maps phenomena, contributions, and problems to the hierarchy.  ...  of any multicellular organism, a hint on the importance of these communication channels.  ... 
arXiv:2009.00090v1 fatcat:5fhpk7dpmvc35b44ysr4srqbc4

Robustness and lethality in multilayer biological molecular networks

Xueming Liu, Enrico Maiorino, Arda Halu, Kimberly Glass, Rashmi B. Prasad, Joseph Loscalzo, Jianxi Gao, Amitabh Sharma
2020 Nature Communications  
of interaction in models of complex biological systems.  ...  AbstractRobustness is a prominent feature of most biological systems. Most previous related studies have been focused on homogeneous molecular networks.  ...  Code availability The main results are generated by using Matlab-R2017a, R-3.6.1, and python 2.7.  ... 
doi:10.1038/s41467-020-19841-3 pmid:33247151 fatcat:bekp3trx3zcfhffmj3xz5shn7e

Technology Assessment 2.0: Revamping Our Approach to Emerging Technologies

Albert Lin
2010 Social Science Research Network  
Synthetic Biology The emerging field of synthetic biology builds on the techniques of conventional genetic engineering and hints at both a wider array of uses as well as more disturbing risks.  ...  of some temperate and respectable body of citizens, in order to check" the potential for misguided and rash decisions by the general public). 106 See ALLAN SCHNAIBERG, THE ENVIRONMENT: FROM SURPLUS  ...  and referendum propositions are on the same ballot, there is on average a fifteen percentage point drop-off in the proportion of voters casting ballots on the latter as compared with the former.  ... 
doi:10.2139/ssrn.1658125 fatcat:qftymakjdvc6lpv2qrrjuand7i

CyanoFactory, a European consortium to develop technologies needed to advance cyanobacteria as chassis for production of chemicals and fuels

Peter Lindblad, David Fuente, Friederike Borbe, Bernardo Cicchi, J. Alberto Conejero, Narciso Couto, Helena Čelešnik, Marcello M. Diano, Marko Dolinar, Serena Esposito, Caroline Evans, Eunice A. Ferreira (+27 others)
2019 Algal Research  
Declaration of author contributions The conception, design, and supervision of the project, and coordination of writing the manuscript, were done by P.  ...  Acknowledgement The collaborate research discussed above received funding from the European Union Seventh Framework Programme (FP7/2007(FP7/ -2013 under the grant agreement number 308518 (project CyanoFactory  ...  Both of these outputs enabled rational design choices to be made based on the intracellular response of the cell, when combined with an in-silico model of the organism.  ... 
doi:10.1016/j.algal.2019.101510 fatcat:ciw3uiqc7vc77f53gewnkyiz4m

Encoded Library Technologies as Integrated Lead Finding Platforms for Drug Discovery

Johannes Ottl, Lukas Leder, Jonas V. Schaefer, Christoph E. Dumelin
2019 Molecules  
Encoded library technologies enable the rapid exploration of large chemical space for the identification of ligands for such targets.  ...  For the identification of low-molecular weight ligands, we apply DNA-encoded libraries. In addition, encoded peptide libraries are employed to identify cyclic peptides.  ...  Model of chemical space available for hit finding and positioning of the encoded library technologies DEL and PDP.  ... 
doi:10.3390/molecules24081629 fatcat:pj4ifdpjoveezmxum2g5oof534

Electroosmosis in nanopores: Computational methods and technological applications [article]

Alberto Gubbiotti, Matteo Baldelli, Giovanni Di Muccio, Paolo Malgaretti, Sophie Marbach, Mauro Chinappi
2022 arXiv   pre-print
Its consequences on the transport properties in biological and synthetic nanopores are subtle and intricate.  ...  Here, we review recent progress on computational techniques for the analysis of electroosmosis and discuss technological applications, in particular for sensing devices.  ...  The authors would also like to thank the researchers that provided us high quality figures, S.L. Zhang Y. Yao for Fig. 2h , G. Maglia and K. Willems for Fig. 3a,d, M . Gracheva for Fig. 3b-c  ... 
arXiv:2111.05786v2 fatcat:sux7sykjhveuhamq5d2nv7ua4i

Modern plant metabolomics: advanced natural product gene discoveries, improved technologies, and future prospects

Lloyd W. Sumner, Zhentian Lei, Basil J. Nikolau, Kazuki Saito
2015 Natural product reports (Print)  
Plant metabolomics has matured and modern plant metabolomics has accelerated gene discoveries and the elucidation of a variety of plant natural product biosynthetic pathways.  ...  In silico fragmentation prediction has been successfully used with compounds consisting of similar repeating units such as peptides, 231 lipids, 226, 232 and glucans. 233, 234 However, its use on  ...  Secondary ions originating from the surface are then generated and used for mass spectral imaging.  ... 
doi:10.1039/c4np00072b pmid:25342293 fatcat:dyyirtbf35eedcadq3qokvlxty

Abstracts from the 26th European Society for Animal Cell Technology Meeting - Cell culture technologies: bridging academia and industry to provide solutions for patients

2020 BMC Proceedings  
Enhanced process understanding and multivariate prediction of the relationship between cell culture process and monoclonal antibody quality.  ...  Acknowledgments This research was partially supported by the developing key technologies for discovering and manufacturing the pharmaceuticals used for next-generation treatments (Japan Agency for Medical  ...  In step 2, a DoE with small-scale semi-continuous perfusion models was applied to optimize the pre-selected feed supplements and to establish valid regression models (B.).  ... 
doi:10.1186/s12919-020-00188-y fatcat:6kscifx565appmxq57svl42biy

Natural Products Modulating Angiotensin Converting Enzyme 2 (ACE2) as Potential COVID-19 Therapies

Murtala Bello Abubakar, Dawoud Usman, Gaber El-Saber Batiha, Natália Cruz-Martins, Ibrahim Malami, Kasimu Ghandi Ibrahim, Bilyaminu Abubakar, Muhammad Bashir Bello, Aliyu Muhammad, Siew Hua Gan, Aliyu Ibrahim Dabai, M Alblihed (+4 others)
2021 Frontiers in Pharmacology  
From a molecular viewpoint, the interaction of SARS-CoV-2 with angiotensin converting enzyme 2 (ACE2) is the crucial first phase of COVID-19 pathogenesis.  ...  Nevertheless, the pandemic is noticeably of lesser burden in African and Asian regions, where the use of traditional herbs predominates, with such relationship warranting a closer look at ethnomedicine  ...  dunal (withanoside X and quercetin glucoside) a In silico NA Molecular modeling/ docking and dynamic simulations Binds receptor binding domain of prefusion spike protein from SARS- CoV-2  ... 
doi:10.3389/fphar.2021.629935 pmid:34012391 pmcid:PMC8126690 fatcat:wmwffk6emzdstgvsjt6axx33we

The Commodification of Emergence: Systems Biology, Synthetic Biology and Intellectual Property

Jane Calvert
2008 BioSocieties  
Drawing on both these examples I explore how ideas about appropriation, including open source, are influencing the nature and course of research in biology.  ...  I start by arguing that commodification and reductionism are closely linked, and that patenting suits entities that are discrete and isolable, such as those that are the focus of molecular biology.  ...  The use of the word 'reduced' here is interesting, and hints of the links between reductionism and commodification.  ... 
doi:10.1017/s1745855208006303 fatcat:5xojqmh4l5cbvifgybxpzpdw6u

In Silico Modeling of the Immune System: Cellular and Molecular Scale Approaches

Mariagrazia Belfiore, Marzio Pennisi, Giuseppina Aricò, Simone Ronsisvalle, Francesco Pappalardo
2014 BioMed Research International  
For the investigation of the physiology and pathology of the immune responses, computer and mathematical models have been used in the last decades, enabling the representation of biological processes.  ...  In this modeling effort, a major issue is represented by the communication between models that work at cellular and molecular level, that is, multiscale representation.  ...  Acknowledgments The authors would like to thank Gerda Therese Ludwig for the helpful suggestions in revising the paper.  ... 
doi:10.1155/2014/371809 pmid:24804217 pmcid:PMC3997136 fatcat:6ynhk46pljeqplcm4cegankvem

Cloud-Based High Throughput Virtual Screening in Novel Drug Discovery [chapter]

Abdurrahman Olğaç, Aslı Türe, Simla Olğaç, Steffen Möller
2019 Msphere  
Drug discovery and development requires the integration of multiple scientific and technological disciplines in chemistry, biology and extensive use of information technology.  ...  Virtual screening (VS) is one of the most often applied CADD methods used in rational drug design, which may be applied in early stages of drug discovery pipeline.  ...  None of the in silico molecular modeling techniques can generate perfect models for all kinds of biochemical processes. However, a large variety of tools is provided by the scientific community.  ... 
doi:10.1007/978-3-030-16272-6_9 fatcat:dihdpicowrg4vbsirumu3o4ezi

Integration of Complex Data Sources to Provide Biologic Insight into Pulmonary Vascular Disease (2015 Grover Conference Series)

Evan L. Brittain, Stephen Y. Chan
2016 Pulmonary Circulation  
The use of -omics platforms, in silico modeling of gene networks, and linkage of large human cohorts with DNA biobanks are beginning to bear biologic insight into pulmonary hypertension.  ...  These approaches to high-throughput molecular phenotyping offer the possibility of discovering new therapeutic targets and identifying variability in response to therapy that can be leveraged to improve  ...  13 Thus, there exists a pressing need to distill critical insight from the volumes of molecular data derived from human tissue for application to clinical and therapeutic use.  ... 
doi:10.1086/686995 pmid:27683602 pmcid:PMC5019078 fatcat:ektohemdgngk3kwjsxp5xiwmaa

Uncovering New Drug Properties in Target-Based Drug-Drug Similarity Networks

Lucreţia Udrescu, Paul Bogdan, Aimée Chiş, Ioan Ovidiu Sîrbu, Alexandru Topîrceanu, Renata-Maria Văruţ, Mihai Udrescu
2020 Pharmaceutics  
Using an energy-model network layout, we generate drug communities associated with specific, dominant drug properties.  ...  DrugBank confirms the properties of 59.52% of the drugs in these communities, and 26.98% are existing drug repositioning hints we reconstruct with our DDSN approach.  ...  Specifically, for pharmacological property φ, we take into consideration the targets from DrugBank that interact with the drugs in the hinted drug d φ h community C x having property φ (T φ x ), and the  ... 
doi:10.3390/pharmaceutics12090879 pmid:32947845 pmcid:PMC7557376 fatcat:v6ehsj56fbdnxj57geswgkgmii
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